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Description: Human interference in estuaries has led to increasing problems of mud, such as hyper-turbidity with adverse ecological effects and siltation of navigation channels and harbours. To deal with this mud sustainably, it is important to understand its long-term effects on the morphology and dynamics of estuaries. The aim of this study is to understand how mud affects the morphological evolution of estuaries. We focus on the effects of fluvial mud supply on the spatial distribution of mudflats and on how this influences estuary width, depth, surface area and dynamics over time. Three physical experiments with self-forming channels and shoals were conducted in a new flume type suitable for tidal experiments: the Metronome. In two of the experiments, we added nutshell grains as mud simulant, which is transported in suspension. Time-lapse images of every tidal cycle and DEMs for every 500 cycles were analysed for the three experiments. Mud settles in distinct locations forming mudflats on bars and sides of the estuary, where the bed elevation is higher. Two important effects of mud were observed: the first is the slight cohesiveness of mud that causes stability on bars limiting vertical erosion, although the bank erosion rate by migrating channels is unaffected. Secondly, mud fills inactive areas and deposits at higher elevations up to the high water level and therefore decreases the tidal prism. These combined effects cause a decrease in dynamics in the estuary and lead to near-equilibrium planforms that are smaller in volume and especially narrower upstream with increased bar heights and no channel deepening. This trend is in contrast with channel deepening in rivers by muddier floodplain formation. These results imply large consequences for long-term morphodynamics in estuaries that become muddier due to management practices, which deteriorate ecological quality of intertidal habitats but may create potential area for marshes.